RetrogeneDB ID: retro_pvam_1302

Retrocopy location

• Organism: Megabat (Pteropus vampyrus)
• Coordinates: scaffold_591:288649..289496(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: PNP
• Ensembl ID: ENSPVAG00000010734
• Aliases: None
• Description: purine nucleoside phosphorylase [Source:HGNC Symbol;Acc:7892]

Sequence

>retro_pvam_1302
CTCGCATATGAAGATTGTCAGAACACTGCAGAATGGCTTCTGTCCCACACTCAAGCACCAACTTCAAGTAGCAGTGATCT
GTGGTTCTGGGTTAGGAGGTTTGACTGATAAATTAACTCTGACCCAGATCTTTGACTACAGTGAGATACCAAACTTCCCC
CAAAGTACAGGGCAAGGTCATGCTGGTCGACTGGTGTTTGAGTTCCTGAATGGCAGAGCCCGTGTGATGATGCAGGGCAA
GATCCACCTGTATGAAGGCTACCTGCTCTGGAAGGTGACATTCCCAGTGAGGGTATTCCAGCTTCTGGCTGTGGACACCC
TAGTGGTCACCAATGCAGCTGGAGGGCTCAAACCCAAGTTTAAGGTTAGAAACATGCTAATCCACGATCACATCAACCTA
CCTGGTCTTTGCAGTGAGAACCCTCACATAGAGCCCAAGGATGAAAGGTTTGGAGTTTGGTTTTCTGCCATGTTTGATGC
CTATCACTGAGAGATGAGGCAGAAGGCTCATAGTACCTGGAGACAAATGAGAGAGCAGAGAGAGCTACAGGAAGGCGCCT
ACGTTATGGTGACGGGCCCCAACTTTGAGACTGTGACAGAGTCTCATCTGCTGCAGAAGCTTGGTGCAGATGCTGTTGGC
ATGAGCACAGTACCAGAAGTTATAGTTGCAAGGCACTGTGGACTTCGAGTCTTTTGCATCTCCCTCTTCACTAACAAGGT
CATCATGGATTGTGAAAGCCTTGAGAAAGCAAACCGTGAAGTACTAAAGACCAGGAAACAAGCTGTGCAGAAATTGGAAC
AGTTTGTCTCCATTCTTATGACTAACATTCCACTGCCTGACCATGCC

Alignment

ORF - retro_pvam_1302 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.97 %
• Parental protein coverage: 98.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTYEDCQYTAEWLLSHT-KHRPQVAVICGSGLGGLTDKLTQTQIFDYSEIPNFPQSTVQGHAGRLVFGFL
          L.YEDCQ.TAEWLLSHT.KH..QVAVICGSGLGGLTDKLT.TQIFDYSEIPNFPQST.QGHAGRLVF.FL
Retrocopy LAYEDCQNTAEWLLSHT>KHQLQVAVICGSGLGGLTDKLTLTQIFDYSEIPNFPQSTGQGHAGRLVFEFL

Parental  NDRACVMMQGRFHLYEGYPLWKFVSKVTFPVRVFQLLGVDTLVVTNAAGGLNPKFEVGDIMLIRDHINLP
          N.RA.VMMQG..HLYEGY.LW....KVTFPVRVFQLL.VDTLVVTNAAGGL.PKF.V...MLI.DHINLP
Retrocopy NGRARVMMQGKIHLYEGYLLW----KVTFPVRVFQLLAVDTLVVTNAAGGLKPKFKVRN-MLIHDHINLP

Parental  GICGENPLIGPNDERYGVRFPAMSDAYDREMRQKAHSAWKQMGEQRELQEGTYVMVAGPSYETVAESRLL
          G.C.ENP.I.P.DER.GV.F.AM.DAY..EMRQKAHS.W.QM.EQRELQEG.YVMV.GP..ETV.ES.LL
Retrocopy GLCSENPHIEPKDERFGVWFSAMFDAYH*EMRQKAHSTWRQMREQRELQEGAYVMVTGPNFETVTESHLL

Parental  QQLGADAVGMSTVPEVIVARHCGLRVFGFSLITNKVIMDYESLEKTNHEEVLKTGKQAAQKLEQFVSILM
          Q.LGADAVGMSTVPEVIVARHCGLRVF..SL.TNKVIMD.ESLEK.N..EVLKT.KQA.QKLEQFVSILM
Retrocopy QKLGADAVGMSTVPEVIVARHCGLRVFCISLFTNKVIMDCESLEKAN-REVLKTRKQAVQKLEQFVSILM

Parental  TSIPLPDHA
          T.IPLPDHA
Retrocopy TNIPLPDHA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq

Pteropus vampyrus was not studied using ChIP-Seq data.

EST

Pteropus vampyrus was not studied using EST data.

TSS

Pteropus vampyrus was not studied using FANTOM5 data.

Lab

retro_pvam_1302 was not experimentally validated.

Homology

Retrocopy orthology:

Pteropus vampyrus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005373	1 retrocopy	retro_amel_1666,
Bos taurus	ENSBTAG00000012317	1 retrocopy	retro_btau_1463,
Choloepus hoffmanni	ENSCHOG00000009274	5 retrocopies	retro_chof_1328, retro_chof_1595, retro_chof_1827, retro_chof_1933, retro_chof_348,
Callithrix jacchus	ENSCJAG00000009676	2 retrocopies	retro_cjac_1195, retro_cjac_1511,
Dasypus novemcinctus	ENSDNOG00000011630	1 retrocopy	retro_dnov_322,
Erinaceus europaeus	ENSEEUG00000002411	1 retrocopy	retro_eeur_541,
Felis catus	ENSFCAG00000006934	1 retrocopy	retro_fcat_1368,
Homo sapiens	ENSG00000198805	1 retrocopy	retro_hsap_2282,
Gorilla gorilla	ENSGGOG00000002126	1 retrocopy	retro_ggor_1695,
Macropus eugenii	ENSMEUG00000014512	3 retrocopies	retro_meug_1282, retro_meug_1560, retro_meug_211,
Macaca mulatta	ENSMMUG00000019126	1 retrocopy	retro_mmul_287,
Mustela putorius furo	ENSMPUG00000018119	2 retrocopies	retro_mputfur_420, retro_mputfur_822,
Nomascus leucogenys	ENSNLEG00000010969	1 retrocopy	retro_nleu_1964,
Otolemur garnettii	ENSOGAG00000013344	4 retrocopies	retro_ogar_1631, retro_ogar_2141, retro_ogar_3083, retro_ogar_594,
Pongo abelii	ENSPPYG00000005567	1 retrocopy	retro_pabe_1938,
Pan troglodytes	ENSPTRG00000006095	1 retrocopy	retro_ptro_1616,
Pteropus vampyrus	ENSPVAG00000010734	1 retrocopy	retro_pvam_1302 ,
Rattus norvegicus	ENSRNOG00000009982	1 retrocopy	retro_rnor_891,
Tupaia belangeri	ENSTBEG00000016378	1 retrocopy	retro_tbel_4632,
Tarsius syrichta	ENSTSYG00000000748	3 retrocopies	retro_tsyr_2057, retro_tsyr_2127, retro_tsyr_235,